|
|
Database: anoCar2 Primary Table: xenoRefSeqAli Row Count: 322,947   Data last updated: 2020-08-18
Format description: Summary info about a patSpace alignment On download server: MariaDB table dump directory
field | example | SQL type | info | description |
bin | 73 | smallint(5) unsigned | range | Indexing field to speed chromosome range queries. |
matches | 1579 | int(10) unsigned | range | Number of bases that match that aren't repeats |
misMatches | 600 | int(10) unsigned | range | Number of bases that don't match |
repMatches | 0 | int(10) unsigned | range | Number of bases that match but are part of repeats |
nCount | 0 | int(10) unsigned | range | Number of 'N' bases |
qNumInsert | 16 | int(10) unsigned | range | Number of inserts in query |
qBaseInsert | 3042 | int(10) unsigned | range | Number of bases inserted in query |
tNumInsert | 24 | int(10) unsigned | range | Number of inserts in target |
tBaseInsert | 98794 | int(10) unsigned | range | Number of bases inserted in target |
strand | +- | char(2) | values | + or - for strand. First character query, second target (optional) |
qName | NM_131862 | varchar(255) | values | Query sequence name |
qSize | 5469 | int(10) unsigned | range | Query sequence size |
qStart | 216 | int(10) unsigned | range | Alignment start position in query |
qEnd | 5437 | int(10) unsigned | range | Alignment end position in query |
tName | chr1 | varchar(255) | values | Target sequence name |
tSize | 263920458 | int(10) unsigned | range | Target sequence size |
tStart | 77486 | int(10) unsigned | range | Alignment start position in target |
tEnd | 178459 | int(10) unsigned | range | Alignment end position in target |
blockCount | 25 | int(10) unsigned | range | Number of blocks in alignment |
blockSizes | 87,127,159,62,131,118,4,108... | longblob | | Size of each block |
qStarts | 216,330,684,849,911,1042,11... | longblob | | Start of each block in query. |
tStarts | 263741999,263742125,2638000... | longblob | | Start of each block in target. |
|
| |
|
|
Connected Tables and Joining Fields
|
|
anoCar2.all_est.qName (via xenoRefSeqAli.qName)
anoCar2.all_mrna.qName (via xenoRefSeqAli.qName)
anoCar2.xenoMrna.qName (via xenoRefSeqAli.qName)
anoCar2.xenoRefFlat.name (via xenoRefSeqAli.qName)
anoCar2.xenoRefGene.name (via xenoRefSeqAli.qName)
hgFixed.gbCdnaInfo.acc (via xenoRefSeqAli.qName)
hgFixed.gbMiscDiff.acc (via xenoRefSeqAli.qName)
hgFixed.gbSeq.acc (via xenoRefSeqAli.qName)
hgFixed.gbWarn.acc (via xenoRefSeqAli.qName)
hgFixed.imageClone.acc (via xenoRefSeqAli.qName)
| |
|
|
Sample Rows
|
|
bin | matches | misMatches | repMatches | nCount | qNumInsert | qBaseInsert | tNumInsert | tBaseInsert | strand | qName | qSize | qStart | qEnd | tName | tSize | tStart | tEnd | blockCount | blockSizes | qStarts | tStarts |
---|
73 | 1579 | 600 | 0 | 0 | 16 | 3042 | 24 | 98794 | +- | NM_131862 | 5469 | 216 | 5437 | chr1 | 263920458 | 77486 | 178459 | 25 | 87,127,159,62,131,118,4,108,3,108,120,165,111,68,117,84,2,111,108,78,126,96,30,25,31, | 216,330,684,849,911,1042,1160,1164,1272,1275,1390,1890,2172,2316,2397,2545,2629,2631,2754,3030,3114,3273,3393,3445,5406, | 263741999,263742125,263800028,263800900,263808257,263808771,263809053,263810191,263810321,263811698,263813028,263819978,26382521 ... |
588 | 612 | 186 | 0 | 0 | 6 | 441 | 11 | 62760 | +- | NM_001267849 | 2728 | 175 | 1414 | chrUn_GL343261 | 2090378 | 454760 | 518318 | 12 | 111,57,39,80,61,69,80,100,120,11,7,63, | 175,358,415,535,615,676,796,876,982,1102,1118,1351, | 1572060,1577662,1579597,1612943,1613535,1622405,1623590,1625195,1632346,1633764,1633777,1635555, |
1296 | 789 | 212 | 0 | 7 | 1 | 72 | 8 | 56450 | ++ | NM_001267811 | 1704 | 541 | 1621 | chr5 | 150641573 | 93238147 | 93295605 | 9 | 121,44,129,98,1,126,132,154,203, | 541,662,706,907,1005,1006,1132,1264,1418, | 93238147,93252057,93278221,93282190,93282304,93285354,93292462,93292843,93295402, |
20 | 449 | 162 | 0 | 1 | 2 | 444 | 7 | 101332 | +- | NM_001267811 | 1704 | 610 | 1666 | chr5 | 150641573 | 93284632 | 93386576 | 8 | 54,42,129,3,153,198,18,15, | 610,664,1132,1261,1264,1417,1633,1651, | 57254997,57268055,57275423,57275572,57279232,57280682,57356505,57356926, |
73 | 1402 | 545 | 0 | 0 | 12 | 1401 | 20 | 96769 | +- | NM_010588 | 4054 | 92 | 3440 | chr1 | 263920458 | 79728 | 178444 | 21 | 81,132,42,249,61,133,116,118,113,3,45,168,90,108,105,120,14,82,2,111,54, | 92,194,386,485,736,797,930,1160,1278,1391,1394,1448,1826,2036,2147,2252,2381,2408,2490,2492,3386, | 263742014,263742125,263742293,263799941,263800899,263808255,263808771,263811695,263813028,263813208,263813604,263815723,26382005 ... |
587 | 246 | 105 | 0 | 0 | 3 | 891 | 3 | 10274 | ++ | NM_024816 | 2307 | 201 | 1443 | chrUn_GL343287 | 1773520 | 379368 | 389993 | 4 | 147,84,45,75, | 201,876,1020,1368, | 379368,383802,384978,389918, |
587 | 272 | 61 | 0 | 0 | 2 | 180 | 2 | 1364 | ++ | NM_005524 | 1575 | 437 | 950 | chrUn_GL343538 | 525768 | 310469 | 312166 | 3 | 81,165,87, | 437,524,863, | 310469,311758,312079, |
585 | 1110 | 427 | 0 | 65 | 9 | 1416 | 14 | 27903 | ++ | NM_145059 | 3907 | 187 | 3205 | chrUn_GL343539 | 474571 | 31731 | 61236 | 15 | 98,58,55,126,23,114,213,156,57,82,120,119,63,77,241, | 187,285,477,721,960,1621,1834,2059,2386,2497,2579,2699,2824,2887,2964, | 31731,33716,37680,41187,43217,51059,52190,52701,53307,54007,55254,56573,56699,60223,60995, |
585 | 752 | 365 | 0 | 0 | 8 | 983 | 9 | 34073 | +- | NM_131861 | 6669 | 686 | 2786 | chr1 | 263920458 | 85291 | 120481 | 11 | 210,42,153,129,99,66,105,118,82,2,111, | 686,1562,1613,1781,1928,2033,2222,2441,2591,2673,2675, | 263799977,263813607,263815723,263819330,263819978,263820077,263825217,263827529,263833640,263833775,263835056, |
1491 | 1015 | 229 | 0 | 22 | 0 | 0 | 8 | 7922 | ++ | NR_156447 | 3943 | 165 | 1431 | chr2 | 199619895 | 118801050 | 118810238 | 9 | 208,132,89,184,119,132,108,150,144, | 165,373,505,594,778,897,1029,1137,1287, | 118801050,118802002,118804041,118806552,118807606,118808456,118808695,118809558,118810094, |
|
Note: all start coordinates in our database are 0-based, not
1-based. See explanation
here.
| |
|
|
|